How to launch GenAP-Pipes analyses?

You will first need to set up your environment before you can launch the pipelines. If you have not done so already, please check our GenAP Pipes User Manual . Once you have followed the instructions, you should be able to launch any pipeline using:


To check the help information for any pipeline use




. To check the help documentation for the Hi-C analysis pipeline ( or the ChIP-Seq analysis pipeline (, try: -h -h 

All our pipelines use the same framework and work in similar ways; each with its own output of course. Once you have learned how to run any pipeline, then you can easily run other pipelines. We have several available toy datasets to help you run the pipelines and practice.

To use most pipelines, you will need two types of files; a Configuration file that stores all the parameters used by the pipeline (extension .ini) and a Readset file that stores all the information about your samples. Some pipelines need a Design file that describes analysis contrasts if needed.

Once all the files are ready, you can launch a pipeline using:

<pipeline_name>.py -c <configuration_files> -r <readset_files> -d <design_file> -s <steps> > script.txt
bash script.txt

To get a better idea, read the documentation about the Readset file, the Design file and launch the pipelines using the toy datasets.

Back to GenAP Pipes User Manual